I've had this issue since the last update and it still is persisting in the new update. The game only seems to read my Wii u pro controller with 8-bitdo and nothing else despite the fact that when I started I was able to set up my Sega Saturn 3D controller via USB adapter. So far I have closed steam and all associated processes, restarted my computer and redownloaded. I've seen other people with similar problems but this may be a larger issue that needs to be patched in by the devs themselves. Speaking of, if anybody knows how to contact them, this is an issue happening with my friends as well and not just me. So if there are no known fixes, please forward this to the devs. Not being able to play with an actual N64 controller is a tragedy considering the context.